Relatedness between major taxonomic groups of fungi based on the measurement of DNA nucleotide sequence homology

Dutta, S. K.; Ojha, Mukti

doi:10.1007/bf01788892

Cited by 48 publications

(25 citation statements)

References 15 publications

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“…In fact, the methylation pattern of locus 16-1 in isolate MZ1-23C was now exactly the VOL. 6,1986 on Table 1) and induced to fruit, and the methylation patterns of random basidiospore isolates were determined. The 5.2-kb HpaII fragment pattern of methylation was stable through dikaryon formation, fruiting, and meiosis.…”

Section: Resultsmentioning

confidence: 99%

Inheritance of DNA methylation in Coprinus cinereus.

Zolan¹,

Pukkila²

1986

Mol. Cell. Biol.

485

212

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We examined the inheritance of 5-methylcytosine residues at a centromere-linked locus in the basidiomycete Coprinus cinereus. Although methylated and unmethylated tracts were inherited both mitotically and meiotically the lengths of these tracts were variable. This variation was not confined to any one phase of the life cycle of the organism, and it usually involved the simultaneous de novo methylation of at least four HpaII-MspI sites. We also found that the higher levels of methylation at this locus were transmitted through meiosis, regardless of the level of methylation of the homologous chromosome.Postreplicative methylation of DNA cytosine residues is a common feature of procaryotic and eucaryotic DNAs. In eucaryotes, cytosine methylation is believed to be a controlling mechanism in gene expression (for examples, see references 5 and 14) and development (7,8). Since most methylation in animals and fungi is at the nucleotide doublet CpG (2, 17), the isoschizomer pair of restriction endonucleases, HpaII and MspI, has provided a powerful tool for the study of the methylation patterns of specific DNA sequences (3, 18). These two enzymes recognize the same sequence (5'-CCGG-3'), but HpaII is sensitive to CpG methylation, while MspI is sensitive to CpC methylation (9).Coprinus cinereus is a particularly useful organism for the study of eucaryotic DNA methylation. This basidiomycete has a small nuclear genome size of 38,000 kilobase pairs (kb) (6), which facilitates molecular analyses. In addition, genetic studies and experimental manipulation of all phases of its life cycle are straightforward and simple. We have shown previously that the nuclear genome of this fungus is extensively methylated at the nucleotide doublet CpG (M. E. Zolan and P. J. Pukkila, in Molecular Genetics of Filamentous Fungi, in press). In that study, we also examined the inheritance of DNA methylation at a centromere-linked locus, termed 16-1, which is methylated in one geographical isolate (Okayama-7) but not in others. Tetrad analysis of progeny from a cross between Okayama-7 and PJP52 (which is unmethylated at 16-1) revealed that methylated tracts are inherited 2:2 during meiosis. That is, progeny that received the chromosome containing locus 16-1 from Okayama-7 were always methylated at that locus, and progeny that inherited locus 16-1 from PJP52 were not methylated at that locus. However, we observed altered lengths of methylated tracts among the methylated progeny. In this study, we asked whether these alterations are a direct consequence of the meiotic process, and we also asked whether the altered tracts resulting from de novo methylation are transmitted as simple Mendelian alleles.MATERIALS AND METHODS C. cinereus strains and growth. The two parents, Okayama-7 and PJP52, of MZ1, the first cross in this study, were described previously (4). The remainder of the strains used were progeny of MZ1 and are described in al. (4). To isolate oidia, 5 ml of sterile H20 was poured onto the surface of a confluent plate of a monokaryotic cultu...

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Section: Resultsmentioning

confidence: 99%

Inheritance of DNA methylation in Coprinus cinereus.

Zolan¹,

Pukkila²

1986

Mol. Cell. Biol.

485

212

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“…The use of DNA sequence variation in fungal evolutionary studies started soon after molecular markers began to be used as tools for assessing relationships between organisms in the early 1970s (Dutta and Ojha 1972). Walker and Doolittle (1982) were the first to use 5S rRNA gene sequences to analyze the relationships among diverse groups of fungi.…”

Section: A Brief History Of Dna Sequence-based Fungal Identificationmentioning

confidence: 99%

Fungal DNA barcoding

2016

Genome

209

149

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Fungi are ubiquitous in both natural and human-made environments. They play important roles in the health of plants, animals, and humans, and in broad ecosystem functions. Thus, having an efficient species-level identification system could significantly enhance our ability to treat fungal diseases and to monitor the spatial and temporal patterns of fungal distributions and migrations. DNA barcoding is a potent approach for rapid identification of fungal specimens, generating novel species hypothesis, and guiding biodiversity and ecological studies. In this mini-review, I briefly summarize (i) the history of DNA sequence-based fungal identification; (ii) the emergence of the ITS region as the consensus primary fungal barcode; (iii) the use of the ITS barcodes to address a variety of issues on fungal diversity from local to global scales, including generating a large number of species hypothesis; and (iv) the problems with the ITS barcode region and the approaches to overcome these problems. Similar to DNA barcoding research on plants and animals, significant progress has been achieved over the last few years in terms of both the questions being addressed and the foundations being laid for future research endeavors. However, significant challenges remain. I suggest three broad areas of research to enhance the usefulness of fungal DNA barcoding to meet the current and future challenges: (i) develop a common set of primers and technologies that allow the amplification and sequencing of all fungi at both the primary and secondary barcode loci; (ii) compile a centralized reference database that includes all recognized fungal species as well as species hypothesis, and allows regular updates from the research community; and (iii) establish a consensus set of new species recognition criteria based on barcode DNA sequences that can be applied across the fungal kingdom.Key words: ITS, secondary barcode, herbarium, metabarcoding, operational taxonomic unit. Résumé :Les champignons sont présents partout, tant dans les environnements naturels qu'anthropisés. Ils jouent des rôles importants dans la santé des plantes, des animaux et des humains de même que dans les écosystèmes. Ainsi, la disponibilité d'un système efficace d'identification des espèces pourrait grandement augmenter la capacité de traiter les maladies fongiques et de surveiller les variations spatiales et temporelles dans la distribution et la migration des champignons. Le codage à barres de l'ADN est une approche potentiellement puissante pour l'identification rapide de spécimens fongiques, permettant d'identifier de nouvelles espèces et guidant les études sur la biodiversité et les écosystèmes. Dans cette mini-synthèse, l'auteur résume brièvement (i) l'histoire de l'identification des champignons sur la base de séquences d'ADN; (ii) l'émergence de la région ITS en tant que code à barre fongique primaire consensuel; (iii) l'emploi des codes à barres ITS pour étudier nombre de questions sur la diversité des champignons de l'échelle locale à globale, inc...

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“…This is particularly true of most of the genera examined in this paper, namely the form-genera within the Hyphomycetes (Barron, 1968 ;Kendrick & Carmichael, 1971) and the Plectomycetes which Fennel1 (1973) admitted was an 'unnatural class '. An extensive analysis of the DNA base composition of fungi by Storck & Alexopoulos (range 47 to 60) respectively, so clearly cannot be distinguished by this method. For genetically based taxonomic relationships, DNA base pairing will probably ultimately provide the best approach (De Ley, 1968), but this has been little exploited by mycologists (Dutta & Ojha, 1972).…”

Section: Discussionmentioning

confidence: 99%

Enzymes of the 3-Oxoadipate Pathway in Fungi: A Serological Study of 3-Carboxymuconate Cyclase (Lactonizing Enzyme) in Fungi and its Possible Taxonomic Significance

Cook

Cain

1977

Journal of General Microbiology

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The immunoglobulin fraction of antiserum prepared against a homogeneous preparation of 3-carboxymuconate cyclase from Aspergillus niger ~6 was used to study the serological relatedness of the enzyme in crude extracts of other fungi. l'mmunodiffusion and immunoelectrophoresis experiments confirmed the homogeneity of the pure A . niger ~6 cyclase, its serological identity with the same enzyme in other strains of A . niger and the complete absence of any cross-reaction with the analogous 3-carboxymuconate cycloisomerase from Pseudomonas putida and Nocardia opaca. Extensive cross-reactions were observed with the cyclases from other species of Aspergillus and Penicillium. When such cross-reactions were examined quantitatively by the precipitin technique, several genera believed to be taxonomically related to Aspergillus and Penicillium on morphological grounds showed crossreacting cyclases. Within the genera there was a broad correlation of serological relationships with morphological subdivisions. These correlations were considerably better than can be achieved by determinations of DNA base compositions because most of the genera examined have GC ratios of 50 to 55 mol %. Crude extracts of two taxonomically unrelated Basidiomycetes showed no serological relatedness to the antisera.

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Relatedness between major taxonomic groups of fungi based on the measurement of DNA nucleotide sequence homology

Cited by 48 publications

References 15 publications

Inheritance of DNA methylation in Coprinus cinereus.

Inheritance of DNA methylation in Coprinus cinereus.

Fungal DNA barcoding

Enzymes of the 3-Oxoadipate Pathway in Fungi: A Serological Study of 3-Carboxymuconate Cyclase (Lactonizing Enzyme) in Fungi and its Possible Taxonomic Significance

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